Correct. Lowering the comprehensive deductible has a nominal impact to the new overall rate.I'm guessing he means because lowering that to $250 or something is cheap.
FYI, my policy has a separate glass deductible. And it's $0. I had the same with Geico and now have All-State. Normally glass claims have a very low deductible. This is a glass claim - make sure they're processing it as such. It might fall into a special category within your glass policy. If your policy has no glass claim category, you might want to switch insurance companies and join the 21st century.